Lab handbook for the Zahn Lab at Utah Valley University
Lab - SB047
Office - SB243c ___ ## Contents
05 What to Expect: A Research Project from Start to Finish
Our mission is to learn new things about the world, to help students develop as scientists and professionals to meet their educational and career goals, to be friendly, and to have fun. Most of the research that takes place in this lab is centered around trying to uncover what the heck microbes are doing, and how we can harness them to useful ends. Experiments can include field studies, manipulated experiments, observational surveys, and/or applied trials. All of this work involves bioinformatics and data analysis.
I’m responsible for everything that goes on in our lab… my goal is to have a lab dedicated not only to uncovering new information about the world, but also to helping you succeed and achieve your academic and professional goals. Your time and effort are valuable to me and I will do my utmost to help you in your work, take your best interests to heart, and direct your efforts in ways that benefit you first and foremost. I will help you learn how research works, how to ask a question, how to get funding, how to collaborate, and how to share your results. I will invest in a friendly and pleasant working environment, with a healthy work/life balance. ___ I’m here to help, but I’m also here to do science, so…
You are responsible for everything you do in the lab. I expect you to be mature, kind to everyone, and work hard. Treat others how you would want to be treated. Enjoy the work…biology is awesome! ___ Here’s a non-comprehensive list of things you should be doing: + Come to lab meetings prepared. + Keep the lab clean. If something is dirty, clean it up! + If you have a lab task, make sure to do it in a timely and diligent manner. + Apply for all available fellowships and grants. Take the initiative to find new ones. + Stay organized. Plan your experiments so you don’t just wander around, keep track of everything in a lab notebook, try to be aware of your whole project. + It’s a micro lab space. It seriously needs to be kept clean. Wipe surfaces with alcohol. All the time. Be crazy clean or all our work will suffer.
And here’s a non-comprehensive list of things can can get you asked to leave the team: + Regularly missing lab meetings + Repeatedly leaving messes in the lab + Leaving the -80 freezer door unlocked and open + Harassment/bullying of other team members + Trying to hide a mistake/accident/spill/error instead of informing me or fixing it + Using supplies from other lab groups without their permission. You need something? I’ll find funding and we will buy it.
Learning to pipette DNA or grow fungi is one thing. Learning how to actually turn data into knowledge is another. Especially for those of you wanting to go to grad school, I’d strongly recommend learning about data analysis. I teach a course for beginners — BIOL 3100 - Introduction to Data Analysis for Biologists — Yes, it’s self-serving that I convince you to take it, and no, you don’t have to. But it’s very useful.
I believe in open and reproducible science, and that means that at least during your time with the lab, so do you. All of our analyses are done using computer code and our raw data are shared freely at publication. If you want to be at the heart of a project from start to finish, you will need to know some basic coding skills. I recommend the R language as that is what I (and most ecologists) use.
We will strive to have regular lab meetings. Sometimes these will be to practice a presentation. Sometimes, they will be to discuss methods or a journal article. You need to come to these regularly to keep me updated on your project’s progress. If you have an assignment for lab meeting (e.g., a paper to read), come prepared.
All of our electronic communication is done on various Slack channels. This helps keep important announcements, etc. all in one place. If you want to share a gif of a cat riding a turtle, that is most excellent, but keep it to the #random channel and off of the main #mycology channel or your project-specific channels. I love it when cats ride turtles, and I love cool photos of mushrooms, but if I have to scroll up for 3 minutes to find the article we need to read for lab meeting, I’m gonna lose my shit.
I try to be available to you whenever I’m around in there. But sometimes my job is to sit quietly and read and write. This is how we get funding and get papers published. Send me a Slack note if you want to stop by. I usually answer those within a few minutes.
You will need to complete Lab Safety Training in order to have keycard access to our lab. (email Craig Moore craig.moore AT uvu DOT edu to set up training) The lab area is shared with other groups. When you walk in, the room on the immediate left (with our poster on it) is our private space. The next door on the left belongs to Dr. G’s lab group. The doors on the right are shared with other lab groups and have lots of equipment you can use. You know how I need you to keep our lab spotlessly clean? Well that goes double for shared spaces! Be a good citizen. + There is a key box in the main lab area. I’ll give you the code to that. The key inside will open all the doors. Don’t use it to open Dr. G’s private lab space door. + In our lab room, there are two refrigerators. The one on the left is for sterile media, soil samples, old mushrooms, snake skins, fingernail clippings and other “dirty” and “living” things. That’s all it is for. The fridge/freezer on the right is for “clean” things: extracted DNA, reagents, PCR products, MagnaBeads, etc. Keep it clean. Don’t ever store live samples in there. + The main incubators in our lab (back left) are for fungal and bacterial cultures. The top incubator is divided into four shelves. Rough and dirty cultures on the bottom, going up to pure cultures ready for DNA extraction on the top. As cultures get cleaned up and isolated, they move up the shelves. + The sterile hood is really annoying sometimes, what with the beeping an such, but it’s a good friend to us. Keep it clean! After every use, wipe it down with alcohol and turn on the UV light. If you want to use the sterilizer, be sure that both it and the fume hood electric power buttons are on. Don’t leave the sterilizer on for more than 3 hours at a time. + If there is a bunch of dirty glassware in the sink, I’m going to lose my shit. Clean up. + The -80 freezer is out through the back door of the lab. Sometimes students will be having class in that room. That’s okay, just don’t be distracting to them. The freezer itself is LOCKED. It needs to stay locked. If you leave it open on accident it can ruin everybody’s samples and reagents. If you do this, it’s probably best for you to run and hide forever! + Any live cultures or pipette tips with biological material on them need to go in the biohazard trash bin next to the lab, rather than the regular trash. + Wear gloves and sterilize them with alcohol. + Follow the lab safety rules you learned in training. + Label your tubes and plates, for the love of all that is holy! + Use your lab notebook (initial and date). No matter what. It goes in the notebook… or it didn’t happen.
You have a few options when you are part of this lab group: + You can volunteer in the lab. If you go this route, you’re not earning credit or money (see below), but that doesn’t mean you don’t have to attend lab meetings or clean up after yourself. There’s a looong list of students eager to get research experience. If you start slacking off, I’ll have to let you move on and someone else will take your place. + You can receive course credit through BIOL489R. Up to 4 credit hours can count towards graduation. Research credit looks good on a transcript. If you want this option, just come talk with me about it and we can decide how to proceed. Keep in mind that you will receive a grade for this. Leaving messes in the lab, missing deadlines, or generally slacking off will be reflected in your grade. Also, keep in mind that 1 credit hour means working 4 hours per week minimum. + You can get yourself paid to do lab work. This will involve some planning ahead since we will need to write a grant. See below for resources about internal funding opportunities. I’ll gladly help you write a grant for wages, but it can take a couple of months and you will need to have a solid project plan in place. This might not be the best option if you are just getting started. You can work up to 28 hours/week and earn $12/hour as a student employee, but internal grants tend to have hard limits on the maximum payout. Still, if you want to focus on research and cut down hours at another job, this will help ease your financial burden.
Our lab runs on hard work, but also on money. The equipment and materials we need for our projects are very expensive and so we need to be vigilant about applying for funding opportunities when they arise. Needless to say, having a grant funded as an undergraduate student looks very good on your CV. I expect you to apply for grants, and will do everything I can to make sure you get them.
Here are some internal UVU funding opportunities you can apply for- https://www.uvu.edu/undergrad-research/student-research/apply-for-funding/ Most of these can be used for equipment and/or wages for you. You’ll have to strike a balance though. If you write one for wages but no equipment, you can’t exactly do much. Better go ahead and apply to several so you can get both. Come talk to me and let’s apply! If you have an idea for a different (external) grant and want to work together on it, that sounds awesome. Let’s do it.
Here’s an Excel-compatible yearly calendar showing approximate due dates at UVU and some conferences so you can plan out your applications: https://github.com/gzahn/Protocols/raw/master/UVU_Student_Grants_Timeline.ods
What’s the point of doing science if you’re not going to share your exciting results with others!? I expect that you will attend at least one conference to share your work. There are plenty of local, national, or international conferences to select from. If you want to travel to a conference, that means we need to find funding. Presntations look good in your CV, and if you are a fan of paperwork, they can mean a free or very cheap trip to somewhere cool.
You usually have a choice, depending on the abstract you submit and the conference to which you submit it. Talks are typically 15 minutes of hell. Posters are usually 2 hours of boredom. I’ll work with you leading up to any conference to make sure you know what you’re doing. You’ll have feedback on your talk/poster, a chance to practice it in lab meetings, and help with designing slides/posters. I’m of the opinion that “less is more” when it comes to this stuff. We will get to that when the time comes.
My goal for each student in my lab is to get authorship on a publication before they leave. This is easier said than done, but if you are willing to work and be persistent, it will happen for you. Authorship is not guaranteed, however. To be an author, you need to substantially contribute to a manuscript. That can take several forms: 1. Collecting the bulk of samples or data for a project 2. Performing data analysis and contributing toward manuscript figures 3. Writing and revising drafts of a manuscript
Each student ideally will develop their own project once they get used to lab procedures and have done the background reading in their area (I’ll help you find the papers but I can’t read them for you). You have initial claim to 1st authorship on any papers from your personal project. Of course, if you flake out and somebody else takes up the slack, it becomes their paper.
This depends on your topic, obviously. But I’ll include a partial list of some papers below that should give you a feel for the sorts of research questions and methods you’ll find in our lab. Wait! holy crap, that’s a lot of reading! Yeah, remember you signed up for this. Get used to it. First, read all the one’s titled “Ten simple rules …” and then move on to the rest.
We will use Zotero to manage papers and citations https://www.zotero.org/. Look it up and learn how to use it.